This GitHub repository contains the code used to process the images acquired using Micro-Manager before subsequent manual analysis. This version of the pipelin takes as input a MicroManager folder and outputs concatenated movies (one per position).

• Raw (input) data: raw data is available on Zenodo (upon publication): URL
• Concatenated (output) data:
  • a series of TIFF, 16-bit files, with appropriate (ImageJ-readable) pixel sizes and timestamp overlays
  • a series of .xls, machine-readable files, with timestamp information.
  • available on Zenodo (upon publication): URL

1. Use Python 3.
2. A working Fiji installation.
3. Use pip to install the missing libraries. We recommend running these scripts in a virtual environment.

pip install numpy pandas scipy matplotlib scikit-image

.cfg files are present in the config/ folder. They contain the parameters used by the script to concatenate the data. It has to be used together with the raw data mentioned above, located in the Zenodo repository.

This file contains most of the user-tunable parameters required to run the pipeline.

• prefix_dict: the root of the folder architecture. Within this folder, the raw MicroManager folders should be located in a data/ subfolder, the concatenated files will be created in the data/Maxime/concatenation/ subfolder. Make sure that these folders exist. The script can be shared between computers, one entry of the dictionary corresponds to one machine.
• fiji_dict: the path to the Fiji executable

Maxime Woringer, with inputs from multiple authors & collaborators, and limited & credited Stack Overflow copy-pasting.

GPLv3+, see the LICENSE file included in this repository for more details.